Jon, it sounds like you took the Main Trail.
The "MR conditions" refers to the Mountaineers Route, which is the non-trail route up the North Fork of Lone Pine Creek. That route splits off at the first main stream crossing, about a half hour from the trail head.
How sore were your feet with the trail runners? What brand, style??
Woops sorry about that

. My feet felt great. I had a brand new pair of New Balance 461 with a $4.50 pair of walmart thin gel insoles under the included ones. I also wore sock liners inside mid-weight hiking socks which likely helped. The only thing killing me after this hike is my calfs.